The invention discloses a method for preparing calcium amino acid, including the preparation of a culture liquid which consists of fish bone powder and enzymolysis protein liquid and the inoculation of lactobacillus acidophilus and streptococcus thermophilus in the culture liquid, then a fermentation liquid which consists of the fish bone powder and the enzymolysis protein liquid is prepared; the mixture of the lactobacillus acidophilus culture liquid and the streptococcus thermophilus culture liquid are inoculated into the fermentation liquid for fermentation, and the fermentation liquid is treated with centrifugation to obtain a yellow calcium amino acid clear liquid. The invention takes tilapia processing offcut-fish bone as main raw material by the combination of the enzymolysis and microbial fermentation; the enzymolysis protein liquid which is prepared by enzymolysis is taken as a protein source, the calcium in the fish bone is freed to be combined with the amino acid in the enzymolysis protein liquid to form the ionic-state calcium amino acid by the fermentation of the lactobacillus acidophilus and the streptococcus thermophilus. The invention can not only high-value utilize the tilapia processing offcut, but also can improve the processing utilization ratio of the tilapia.